# 🥉 Contribution ## Education We have noticed an elevated interest in bioinformatic methods and lack of teaching and practicing for non-specialised students. We believe that in silico analysis will gain more and more user trust, as the technology and algorithms advance. > To address this challenge, we have developed three guides on the basics of bioinformatic tools. We are glad to share the Russian versions with our colleagues from former USSR republics, where, in our experience, they are very much needed. **The English versions will be available shortly. ** - [BLAST_guide_RU.pdf](https://static.igem.org/mediawiki/2021/b/be/T--LMSU--guide_blast.pdf) - [MEGA_guide_RU.pdf](https://static.igem.org/mediawiki/2021/2/2e/T--LMSU--guide_mega.pdf) - [PyMol_guide_RU.pdf](https://static.igem.org/mediawiki/2021/2/2f/T--LMSU--guide_pymol.pdf) ## General advice We have thought a lot about protein dynamics modelling and its role in the success of an iGEM project. Protein fusion is a desired tool for synthetic biology, which can be spplied in fields of: - pathway optimisation via protein colocalization; - designing biosensors using readily available parts; - estimating stability of novel DNA binding proteins. - in our case, combining two photoreceptor proteins for ensured accuracy and selectivity. We offer a comprehensive follow-through pipeline on protein dynamics modelling, from sequence to potential energy estimates and visualisation. The guide can be found [here](https://static.igem.org/mediawiki/2021/4/46/T--LMSU--MD-Principles-Guide.pdf) > We hope that our approach and our tool selection is the most useful and easy-to-use with minimal knowledge of bioinformatics. ## Strain characterization ### Physiology This year we've been meaning to address the issue of underrepresentation of biological chassis organisms in the iGEM competition. Our long-term goal is to propose the Arhtrospira platensis as a potent biotechnological organism. This year we have done the physiological, nutritional and biochemical analysis of IPPAS B-256 strain. We analyzed several cultivation parameters such as temperature, light coditions, and pH. The optimal conitions are: - СО2 source (gas-air mix): 1,5-2 % СО2 - Temperature: 32ºС - Lighting: twenty-four hour - Illumunation: 500 µmol photon light m2s-1 - Type of lamps: one-sided, LED white, red, blue Please feel free to observe more data in /Results and /Protocols sections. For these conditions the growth constant was determined for future organism growth modeling applications. > We hope that the acquired data will facilitate our and other teams' effort to work with this organism. ![https://static.igem.org/mediawiki/2021/c/c5/T--LMSU--Team_LMSU_photobioreactor.jpeg] ### Biochemistry We have determined the nutritional value of A. platensis. Microalgae can switch between storage compounds when limited by a nutrient. The nitrogen and phosphorus starvation conditions were studied, because these were shown to induce the accumulation of starch or lipids in other microalgae. The results on control biomass are available on the /Results page, and the starvation nutritional values will be available shortly. > This data can be used to estimate the production of desired compounds and possible food applications. ### Genetics The protocol for genomic DNA extraction was optimised. Main additions are the cell disintegration and DNA purification protocols. Fragments of interest can be PCR amplified successfully. > This may help other teams who choose to work with the suggested organism to investigate or control the region of interest, if any. ![https://static.igem.org/mediawiki/2021/c/cf/T--LMSU--gDNA_pcr.jpeg]
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